Merge pull request #1571 from glotzerlab/release-4.0

Release 4.0
glotzerlab · Jun 6, 2023 · 87c0509 · 87c0509
2 parents 40153e6 + 17dc067
commit 87c0509
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.11.0
+current_version = 4.0.0
 commit = False
 tag = False
 parse = ^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P<number>0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -62,7 +62,7 @@ body:
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 3.11.0
+      placeholder: 4.0.0
     validations:
       required: true
   - type: markdown
@@ -73,7 +73,7 @@ body:
     attributes:
       label: Python version
       description: What version of Python are you using?
-      placeholder: 3.10.6
+      placeholder: 3.11.3
     validations:
       required: true
   - type: markdown

diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md
@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release v3.x.y'
+title: 'Release 4.x.y'
 labels: ''
 assignees: 'joaander'
 

diff --git a/.mailmap b/.mailmap
@@ -72,6 +72,7 @@ Alyssa Travitz <[email protected]>
 Ross Smith <[email protected]>
 Tim Moore <[email protected]> Tim Moore <[email protected]>
 Tim Moore <[email protected]> Tim Moore <[email protected]>
+Tim Moore <[email protected]> mtimc <[email protected]>
 Aaron Keys <[email protected]>
 Brandon Denis Smith <[email protected]> Brandon Denis Smith <bradenis@brandon-work.(none)>
 Igor Morozov <[email protected]>
@@ -127,6 +128,7 @@ Peter Schwendeman <[email protected]> Peter S. Schwendeman <[email protected]>
 Philipp Schönhöfer <[email protected]> Philipp Schönhöfer <[email protected]>
 Philipp Schönhöfer <[email protected]> SchoeniPhlippsn <[email protected]>
 Philipp Schönhöfer <[email protected]> Philipp Schönhöfer <[email protected]_w_724v_typ_a_05011603_06_003>
+Philipp Schönhöfer <[email protected]> SchoeniPhlippsn <[email protected]>
 Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]>
 Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]>
 Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]>
@@ -158,3 +160,9 @@ Chris Jones <[email protected]> <[email protected]>
 Melody Zhang <[email protected]> Melody Zhang <[email protected]>
 Jen Bradley <[email protected]> Jen Bradley <[email protected]>
 Jen Bradley <[email protected]> janbridley <[email protected]>
+Martin Girard <[email protected]> MartinGirard <[email protected]>
+Martin Girard <[email protected]> martin <[email protected]>
+Ignacio Blanco Varela <[email protected]> Ignacio Blanco Varela <[email protected]>
+Domagoj Fijan <[email protected]> Domagoj Fijan <[email protected]>
+Domagoj Fijan <[email protected]> Domagoj Fijan <[email protected]>
+Adrien Chen <[email protected]> Adrien Chen <[email protected]>
diff --git a/BUILDING.rst b/BUILDING.rst
@@ -145,7 +145,7 @@ Clone using Git_::
 
    $ git clone --recursive https://github.com/glotzerlab/hoomd-blue
 
-Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-v3.11.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-v4.0.0.tar.gz`_.
 
 .. seealso::
 
@@ -158,7 +158,7 @@ Release tarballs are also available as `GitHub release`_ assets: `Download hoomd
     Execute ``git submodule update --init`` to fetch the submodules each time you switch branches
     and the submodules show as modified.
 
-.. _Download hoomd-v3.11.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v3.11.0/hoomd-v3.11.0.tar.gz
+.. _Download hoomd-v4.0.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.0.0/hoomd-v4.0.0.tar.gz
 .. _GitHub release: https://github.com/glotzerlab/hoomd-blue/releases
 .. _git book: https://git-scm.com/book
 .. _Git: https://git-scm.com/

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,11 +4,11 @@
 Change Log
 ==========
 
-v4.x
-----
+4.x
+---
 
-v4.0.0 (not yet released)
-^^^^^^^^^^^^^^^^^^^^^^^^^
+4.0.0 (2023-06-06)
+^^^^^^^^^^^^^^^^^^
 
 *Fixed*
 
@@ -18,6 +18,8 @@ v4.0.0 (not yet released)
   (`#1548 <https://github.com/glotzerlab/hoomd-blue/pull/1548>`__).
 * Work around cases where Python's garbage collector fails to collect ``Operation`` objects
   (`#1457 <https://github.com/glotzerlab/hoomd-blue/issues/1457>`__).
+* Incorrect behavior with ``hpmc.external.user.CPPExternalPotential`` in MPI domain decomposition
+  simulations (`#1562 <https://github.com/glotzerlab/hoomd-blue/issues/1562>`__).
 
 *Added*
 
@@ -38,6 +40,16 @@ v4.0.0 (not yet released)
   (`#1541 <https://github.com/glotzerlab/hoomd-blue/pull/1541>`__).
 * More descriptive error messages when calling ``Simulation.run``
   (`#1552 <https://github.com/glotzerlab/hoomd-blue/pull/1552>`__).
+* `hoomd.Snapshot.from_gsd_frame` - convert a `gsd.hoomd.Frame` object to `hoomd.Snapshot`
+  (`#1559 <https://github.com/glotzerlab/hoomd-blue/pull/1559>`__).
+* `hoomd.device.NoticeFile` - a file-like object that writes to `hoomd.device.Device.notice`
+  (`#1449 <https://github.com/glotzerlab/hoomd-blue/issues/1449>`__).
+* `hoomd.write.Burst` - selective high-frequency frame writing to GSD files
+  (`#1543 <https://github.com/glotzerlab/hoomd-blue/pull/1543>`__).
+* Support LLVM 16
+  (`#1568 <https://github.com/glotzerlab/hoomd-blue/pull/1568>`__).
+* More detailed status message for found CUDA libraries
+  (`#1566 <https://github.com/glotzerlab/hoomd-blue/pull/1566>`__).
 
 *Changed*
 
@@ -68,12 +80,16 @@ v4.0.0 (not yet released)
   (`#1538 <https://github.com/glotzerlab/hoomd-blue/pull/1538>`__).
 * No longer test with GCC 7-8, Python 3.6-3.7, or Clang 6-9)
   (`#1544 <https://github.com/glotzerlab/hoomd-blue/pull/1544>`__).
+* Improved error messages with NVRTC compiled code
+  (`#1567 <https://github.com/glotzerlab/hoomd-blue/pull/1567>`__).
 
 *Deprecated*
 
 * ``Scalar``, ``Scalar2``, ``Scalar3``, and ``Scalar4`` data types. Use ``LongReal[N]`` instead in
   new code
   (`#355 <https://github.com/glotzerlab/hoomd-blue/issues/355>`__).
+* ``hoomd.Snapshot.from_gsd_snapshot`` - use `hoomd.Snapshot.from_gsd_frame`
+  (`#1559 <https://github.com/glotzerlab/hoomd-blue/pull/1559>`__).
 
 *Removed*
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "3.11.0")
+set(HOOMD_VERSION_RAW "4.0.0")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

diff --git a/example_plugins/CMakeLists.txt b/example_plugins/CMakeLists.txt
@@ -6,7 +6,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 3.9 FATAL_ERROR)
 project(example_plugins LANGUAGES C CXX)
 
 # Find the installed HOOMD
-find_package(HOOMD 3.0.0 REQUIRED)
+find_package(HOOMD 4.0.0 REQUIRED)
 
 message(STATUS "Found HOOMD ${HOOMD_VERSION}: ${HOOMD_INSTALL_PREFIX}/${PYTHON_SITE_INSTALL_DIR}")
 

diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py
@@ -67,9 +67,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v3.11.0/hoomd/VectorMath.h
+            v4.0.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v3.11.0/hoomd/BoxDim.h
+            v4.0.0/hoomd/BoxDim.h
 
     Example:
         .. code-block:: python

diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py
@@ -75,7 +75,7 @@ class CPPPotentialBase(AutotunedObject):
                 HOOMD-blue source code.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v3.11.0/hoomd/VectorMath.h
+            v4.0.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.

diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py
@@ -63,8 +63,8 @@
 copyright = f'2009-{ year } The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '3.11.0'
-release = '3.11.0'
+version = '4.0.0'
+release = '4.0.0'
 
 language = 'en'
 

diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial
+17 −4		.github/workflows/test.yml
+1 −1		.pre-commit-config.yaml
+1 −1		00-Introducing-HOOMD-blue/00-index.ipynb
+1 −1		00-Introducing-HOOMD-blue/01-The-Simulation-Object.ipynb
+1 −1		00-Introducing-HOOMD-blue/02-Performing-Hard-Particle-Monte-Carlo-Simulations.ipynb
+18 −18		00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb
+9 −8		00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb
+7 −7		00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb
+28 −8		00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb
+1,044 −13		00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.ipynb
+576 −10		01-Introducing-Molecular-Dynamics/01-Molecular-Dynamics-Simulations.ipynb
+27 −24		01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb
+874 −14		01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb
+1,019 −98		02-Logging/01-Logging-to-a-GSD-file.ipynb
+1,768 −40		02-Logging/02-Saving-Array-Quantities.ipynb
+14 −11		02-Logging/03-Storing-Particle-Shape.ipynb
+40 −34		02-Logging/04-Writing-Formatted-Output.ipynb
+1 −1		03-Parallel-Simulations-With-MPI/00-index.ipynb
+13 −18		03-Parallel-Simulations-With-MPI/01-Introduction-to-MPI.ipynb
+36 −30		03-Parallel-Simulations-With-MPI/02-Domain-Decomposition.ipynb
+6 −4		03-Parallel-Simulations-With-MPI/03-Accessing-System-Configurations-With-MPI.ipynb
+8 −6		03-Parallel-Simulations-With-MPI/04-Running-Multiple-Simulations-With-Partitions.ipynb
+2 −4		03-Parallel-Simulations-With-MPI/domain_decomposition.py
+4 −2		03-Parallel-Simulations-With-MPI/lj_domain_error.py
+4 −2		03-Parallel-Simulations-With-MPI/lj_kinetic_energy.py
+5 −3		03-Parallel-Simulations-With-MPI/lj_partition.py
+5 −3		03-Parallel-Simulations-With-MPI/lj_performance.py
+4 −2		03-Parallel-Simulations-With-MPI/lj_trajectory.py
+1 −1		04-Custom-Actions-In-Python/02-An-Initial-Custom-Action.ipynb
+1 −1		04-Custom-Actions-In-Python/03-Custom-Action-Features.ipynb
+6 −5		04-Custom-Actions-In-Python/04-Custom-Updater.ipynb
+1 −1		04-Custom-Actions-In-Python/05-Custom-Writer.ipynb
+7 −6		04-Custom-Actions-In-Python/06-Improving-Performance.ipynb
+12 −12		05-Organizing-and-Executing-Simulations/01-Organizing-Data.ipynb
+94 −30		05-Organizing-and-Executing-Simulations/02-Executing-Simulations.ipynb
+58 −29		05-Organizing-and-Executing-Simulations/03-Continuing-Simulations.ipynb
+36 −37		05-Organizing-and-Executing-Simulations/04-Submitting-Cluster-Jobs.ipynb
+5 −6		05-Organizing-and-Executing-Simulations/project.py
+7 −8		05-Organizing-and-Executing-Simulations/project_partitioned.py
+946 −31		06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb
+15 −17		06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb
+5 −8		06-Modelling-Rigid-Bodies/03-Preparing-a-General-Body.ipynb
+1,070 −993		07-Modelling-Patchy-Particles/02-Simulating-a-System-of-Patchy-Particles.ipynb